Bayern manager Hansi Flick sent on Niklas Sule as his replacement on 25 minutes.
Boateng had taken a late fitness test before the game but could not complete the half.
Bayern Munich were drawing 0-0 with Paris St Germain at halftime in the Champions League final on Sunday after an absorbing first period in which the French side looked more threatening but both teams came close to scoring.
Kylian Mbappe missed a glorious chance to give PSG the lead on the stroke of half time but shot straight at Bayern keeper Manuel Neuer, who had made a superb double save to thwart Neymar earlier on.
At the other end, Bayern's top scorer Robert Lewandowski fired against the post and then headed straight at keeper Keylor Navas.
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